Figure 3

Conformational clusters of the G domain loops of (a) \(\hbox {mGBP2}_{\mathrm{apo}}\), (b) \(\hbox {mGBP2}_{\mathrm{GTP}}\), and (c) \(\hbox {mGBP2}_{\mathrm{holo}}\) as well as (d) for the geranylgeranyl anchor. (a–c) In the upper panels, the central conformations for the five most populated clusters (or fewer if \(<5\) were found) are shown in opaque and for the other clusters in transparent, using different colors for the different loops as specified in the figures. For \(\hbox {mGBP2}_{\mathrm{GTP}}\) and \(\hbox {mGBP2}_{\mathrm{holo}}\), the GTP-binding pocket is indicated by showing GTP and \(\hbox {Mg}^{2+}\) (in transparent green and light orange). The helix \(\alpha 4\)’ is also highlighted in light red. The homology model of mGBP2 is shown as reference in a gray cartoon representation. In the lower panels, the different conformations of key residues for all clusters are shown, as sticks colored according to their residue type (white: apolar; green: polar; blue: positively charged; red: negatively charged), and labeled. (d) The central cluster conformations of the geranylgeranyl group (GG, magenta sticks) of \(\hbox {mGBP2}_{\mathrm{holo}}\) are shown in opaque for the three most populated clusters and in transparent for all other clusters. The initial conformation of the geranylgeranyl group used to start the HREMD simulation is also depicted (gray sticks), while the homology model of the whole protein is presented as cartoon and colored based on residue type as explained in the legend box.